This proposal seeks funding for continuation of our national bio-organic, biomedical mass spectrometry research resource at UCSF. The primary purpose of this program is to advance the detailed molecular knowledge of human biology by infusing powerful, state of the art mass spectrometry-based technologies into important and timely opportunities and challenges in protein, systems and epigenetic biology. In this national center, resource scientists learn the full extent of new collaborator's research needs, the limitations of existing resource methodologies and instrumentation, and thus the real requirements that must drive developments in core methodologies and technologies to solve these important problems. In these close interactions, training of collaborative scientists occurs as well. Key goals include research on the human proteome including neural stem cells, large macromolecular assemblages that are dynamic, functional entities in cells, and the nature and role of posttranslational modulation in cell biology. Particular emphasis is on the discovery and definition of detailed molecular distinctions between normal and aberrant protein function(s). Covalent modifications include phosphorylation, sulfation, O-GlcNAcylation, methylation, acetylation, ubiquitinylation, lipidation, proteolysis and specific chemical cross-linkages. For some classes of proteins, posttranslational occupancies occur in multiple 'combinatorial'motifs that create effector recognition modules, and thus function in a concerted, synergistic manner, e.g. in chromatin biology, the "histone code, the methyl-phos switch, etc." These occupancies are reversible;so knowledge of their alteration by protein complexes that regulate chromatin structure and transcription is sought. Further advances require matching new mass spectrometry and related technologies together with large scale data handling to open more powerful windows to 'see'into the machinery of cells and provide exciting new avenues needed to decipher the true complexity, posttranslational variability and dynamics of functional entities and complex assemblages. On-going and new capabilities include major improvements in reliability of protein identification and quantitation, assignment of sites of covalent modifications with electron capture and transfer dissociation technologies, studies of stoichiometry of intact proteins multiply modified by different moieties, and the power to deal with labile modifications as well as intact proteins using electron capture and electron transfer dissociation. The detailed molecular insights obtainable from new mass spectrometry will continue to have a dramatic impact on gaining a comprehensive understanding of epigenetic regulation of cellular processes. Collaborative topics map onto a wide array of human diseases, including the Down and Angelman syndromes, type II diabetes, signaling complexes in neuron regeneration, X-chromosome silencing, chromatin remodeling, atherosclerotic heart disease, innate immunity, AIDS, parasitic diseases and cancer.